Terminologies augmented recurrent neural network model for clinical named entity recognition

TL;DR

This paper introduces a hybrid neural network model augmented with medical terminologies to improve clinical named-entity recognition in both English and French, achieving near state-of-the-art results.

Contribution

The study presents a novel hybrid system combining terminology-based features with biGRU-CRF for clinical NER, including a new French corpus for diverse clinical entities.

Findings

Hybrid system outperforms standalone models in F-measure.

Terminology augmentation improves performance in low-resource settings.

French corpus APcNER enables effective evaluation of clinical NER in French.

Abstract

We aimed to enhance the performance of a supervised model for clinical named-entity recognition (NER) using medical terminologies. In order to evaluate our system in French, we built a corpus for 5 types of clinical entities. We used a terminology-based system as baseline, built upon UMLS and SNOMED. Then, we evaluated a biGRU-CRF, and an hybrid system using the prediction of the terminology-based system as feature for the biGRU-CRF. In English, we evaluated the NER systems on the i2b2-2009 Medication Challenge for Drug name recognition, which contained 8,573 entities for 268 documents. In French, we built APcNER, a corpus of 147 documents annotated for 5 entities (drug name, sign or symptom, disease or disorder, diagnostic procedure or lab test and therapeutic procedure). We evaluated each NER systems using exact and partial match definition of F-measure for NER. The APcNER contains 4,837 entities which took 28 hours to annotate, the inter-annotator agreement was acceptable for Drug name in exact match (85%) and acceptable for other entity types in non-exact match (>70%). For drug name recognition on both i2b2-2009 and APcNER, the biGRU-CRF performed better that the terminology-based system, with an exact-match F-measure of 91.1% versus 73% and 81.9% versus 75% respectively. Moreover, the hybrid system outperformed the biGRU-CRF, with an exact-match F-measure of 92.2% versus 91.1% (i2b2-2009) and 88.4% versus 81.9% (APcNER). On APcNER corpus, the micro-average F-measure of the hybrid system on the 5 entities was 69.5% in exact match, and 84.1% in non-exact match. APcNER is a French corpus for clinical-NER of five type of entities which covers a large variety of document types. Extending supervised model with terminology allowed for an easy performance gain, especially in low regimes of entities, and established near state of the art results on the i2b2-2009 corpus.